2015-08-13

Paper on "Reliability of pedigree-based and genomic evaluations in selected populations" has finally been published after tedious reviews. This work is a follow up study on reliability of genetic evaluation in selected populations by Piter Bijma (link), but this time connecting pedigree-based and genomic evaluations. The take-home message is that PEV-based reliabilities of genomic predictions are not so much affected by selection as pedigree predictions. This has implications when different breeding program designs are compared using PEV reliabilities - commonly PEV reliability of genomic and pedigree predictions are compared - and suggests that genotyping female selection candidates has been undervalued and should be reconsidered.

2015-03-07

Our new paper titled "Potential of genotyping-by-sequencing for genomic selection in livestock populations" has been published in Genetics Selection Evolution. This work shows that genotypes called from low-coverage sequencing data can be equally or even more powerful for genomic prediction than high-quality SNP genotypes. In particular manipulation of coverage allows us to increase number of genotyped individuals at the expense of genotype quality and this can bring us a long way before accuracy of genomic predictions falls significantly. Another useful application is in increasing selection intensity by genotyping more/all selection candidates.

2013-12-01

Are you using R for data manipulation for later use with other programs, i.e., a workflow something like this:

read data sets from a disk,

modify the data, and

write it back to a disk.

All fine, but of data set is really big, then you will soon stumble on memory issues. If data processing is simple and you can read only chunks, say only line by line, then the following might be useful:

2013-07-02

R can be used also as a scripting tool. We just need to add shebang in the first line of a file (script):

#!/usr/bin/Rscript

and then the R code should follow.

Often we want to pass arguments to such a script, which can be collected in the script by the commandArgs() function. Then we need to parse the arguments and conditional on them do something. I came with a rather general way of parsing these arguments using simply these few lines: